| 🟡 |
bioimageio format validation |
| status |
valid-format |
| source |
https://hypha.aicell.io/bioimage-io/artifacts/straightforward-crocodile/files/rdf.yaml?version=v0 |
| id |
10.5281/zenodo.5910854/6539073 |
| version |
1 |
| applied format |
model 0.4.10 |
| bioimageio.spec |
0.5.7.4 |
|
Location |
Details |
| ✔️ |
|
Successfully created `ModelDescr` instance. |
| ✔️ |
|
bioimageio.spec format validation model 0.4.10 |
| ⚠ |
weights.torchscript.pytorch_version |
missing. Please specify the PyTorch version these Torchscript weights were created with. |
| ✔️ |
weights.onnx |
Found existing conda environment '4d82a6bc4511b4ad0459f190edebc373e2ca235c8452606867e45b1507100a34' |
| ❌ |
weights.onnx |
Reproduce test outputs from test inputs (onnx) |
| ❌ |
weights.onnx |
model.v0_4.ScaleLinearKwargs with axes not implemented, please consider updating the model to v0_5. |
|
|
See Traceback 1. |
|
weights.onnx |
recommended conda environment (Reproduce test outputs from test inputs (onnx)) |
|
|
%YAML 1.2
---
channels:
- conda-forge
- nodefaults
dependencies:
- conda-forge::bioimageio.core
- onnxruntime
- pip
|
|
weights.onnx |
conda compare (Reproduce test outputs from test inputs (onnx)) |
|
|
Success. All the packages in the specification file are present in the environment with matching
version and build string. |
| ❌ |
weights.torchscript |
Conda environment creation |
| ❌ |
weights.torchscript |
Command '['conda', 'env', 'create', '--yes', '--file=/tmp/tmpsnn702v5/torchscript/env.yaml', '--name=8e61e58e234408358ebe72e5f3a59a6fb1adb59db8e7656f72bc034a857c269d', '--quiet']' returned non-zero exit status 1. |
|
|
See Traceback 2. |
|
weights.torchscript |
recommended conda environment (Conda environment creation) |
|
|
%YAML 1.2
---
channels:
- conda-forge
- nodefaults
dependencies:
- conda-forge::bioimageio.core>=0.9.4
- mkl ==2024.0.0
- numpy <2
- pip
- pytorch==1.10.1
- setuptools <70.0.0
- torchaudio==0.10.1
- torchvision==0.11.2
|
|
weights.torchscript |
conda compare (Conda environment creation) |
|
|
bioimageio.core not found mkl not found numpy not found pip not found pytorch not found
setuptools not found torchaudio not found torchvision not found |
Traceback 1
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /usr/share/miniconda/envs/4d82a6bc4511b4ad0459f190edebc373e2ca235c8452606867e45b1507100a34/lib/p │
│ │
│ 781 │ │ test_input = get_test_input_sample(model) │
│ 782 │ │ expected = get_test_output_sample(model) │
│ 783 │ │ │
│ ❱ 784 │ │ with create_prediction_pipeline( │
│ 785 │ │ │ bioimageio_model=model, devices=devices, weight_format=weight_format │
│ 786 │ │ ) as prediction_pipeline: │
│ 787 │ │ │ results = prediction_pipeline.predict_sample_without_blocking(test_input) │
│ │
│ /usr/share/miniconda/envs/4d82a6bc4511b4ad0459f190edebc373e2ca235c8452606867e45b1507100a34/lib/p │
│ │
│ 384 │ │ │ else: │
│ 385 │ │ │ │ yield Sample(members=dict(zip(input_ids, x)), stat=common_stat, id=i) │
│ 386 │ │
│ ❱ 387 │ preprocessing, postprocessing = setup_pre_and_postprocessing( │
│ 388 │ │ bioimageio_model, │
│ 389 │ │ dataset(), │
│ 390 │ │ keep_updating_initial_dataset_stats=keep_updating_initial_dataset_statistics, │
│ │
│ /usr/share/miniconda/envs/4d82a6bc4511b4ad0459f190edebc373e2ca235c8452606867e45b1507100a34/lib/p │
│ │
│ 95 │ """ │
│ 96 │ Get pre- and postprocessing operators for a `model` description. │
│ 97 │ Used in `bioimageio.core.create_prediction_pipeline""" │
│ ❱ 98 │ prep, post, prep_meas, post_meas = _prepare_setup_pre_and_postprocessing(model) │
│ 99 │ │
│ 100 │ missing_dataset_stats = { │
│ 101 │ │ m │
│ │
│ /usr/share/miniconda/envs/4d82a6bc4511b4ad0459f190edebc373e2ca235c8452606867e45b1507100a34/lib/p │
│ │
│ 216 │
│ 217 def _prepare_setup_pre_and_postprocessing(model: AnyModelDescr) -> _SetupProcessing: │
│ 218 │ if isinstance(model, v0_4.ModelDescr): │
│ ❱ 219 │ │ pre = _prepare_procs(model.inputs) │
│ 220 │ │ post = _prepare_procs(model.outputs) │
│ 221 │ elif isinstance(model, v0_5.ModelDescr): │
│ 222 │ │ pre = _prepare_procs(model.inputs) │
│ │
│ /usr/share/miniconda/envs/4d82a6bc4511b4ad0459f190edebc373e2ca235c8452606867e45b1507100a34/lib/p │
│ │
│ 188 │ │ │
│ 189 │ │ if isinstance(t_descr, (v0_4.InputTensorDescr, v0_5.InputTensorDescr)): │
│ 190 │ │ │ for proc_d in t_descr.preprocessing: │
│ ❱ 191 │ │ │ │ procs.append(get_proc(proc_d, t_descr)) │
│ 192 │ │ elif isinstance(t_descr, (v0_4.OutputTensorDescr, v0_5.OutputTensorDescr)): │
│ 193 │ │ │ for proc_d in t_descr.postprocessing: │
│ 194 │ │ │ │ procs.append(get_proc(proc_d, t_descr)) │
│ │
│ /usr/share/miniconda/envs/4d82a6bc4511b4ad0459f190edebc373e2ca235c8452606867e45b1507100a34/lib/p │
│ │
│ 719 │ elif isinstance(proc_descr, v0_5.FixedZeroMeanUnitVarianceDescr): │
│ 720 │ │ return FixedZeroMeanUnitVariance.from_proc_descr(proc_descr, member_id) │
│ 721 │ elif isinstance(proc_descr, (v0_4.ScaleLinearDescr, v0_5.ScaleLinearDescr)): │
│ ❱ 722 │ │ return ScaleLinear.from_proc_descr(proc_descr, member_id) │
│ 723 │ elif isinstance( │
│ 724 │ │ proc_descr, (v0_4.ScaleMeanVarianceDescr, v0_5.ScaleMeanVarianceDescr) │
│ 725 │ ): │
│ │
│ /usr/share/miniconda/envs/4d82a6bc4511b4ad0459f190edebc373e2ca235c8452606867e45b1507100a34/lib/p │
│ │
│ 310 │ │ │ axis = kwargs.axis │
│ 311 │ │ elif isinstance(kwargs, v0_4.ScaleLinearKwargs): │
│ 312 │ │ │ if kwargs.axes is not None: │
│ ❱ 313 │ │ │ │ raise NotImplementedError( │
│ 314 │ │ │ │ │ "model.v0_4.ScaleLinearKwargs with axes not implemented, please consid │
│ 315 │ │ │ │ ) │
│ 316 │ │ │ axis = None │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
NotImplementedError: model.v0_4.ScaleLinearKwargs with axes not implemented, please consider updating the model to v0_5.
Traceback 2
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:428 in _test │
│ │
│ 425 │ │ raise RuntimeError("Conda not available") from e │
│ 426 │ │
│ 427 │ try: │
│ ❱ 428 │ │ run_command([CONDA_CMD, "run", "-n", env_name, "python", "--version"]) │
│ 429 │ except Exception as e: │
│ 430 │ │ working_dir.mkdir(parents=True, exist_ok=True) │
│ 431 │ │ path = working_dir / "env.yaml" │
│ │
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:198 in defau │
│ │
│ 195 │
│ 196 def default_run_command(args: Sequence[str]): │
│ 197 │ logger.info("running '{}'...", " ".join(args)) │
│ ❱ 198 │ _ = subprocess.check_call(args) │
│ 199 │
│ 200 │
│ 201 def test_description( │
│ │
│ /usr/lib/python3.12/subprocess.py:413 in check_call │
│ │
│ 410 │ │ cmd = kwargs.get("args") │
│ 411 │ │ if cmd is None: │
│ 412 │ │ │ cmd = popenargs[0] │
│ ❱ 413 │ │ raise CalledProcessError(retcode, cmd) │
│ 414 │ return 0 │
│ 415 │
│ 416 │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
CalledProcessError: Command '['conda', 'run', '-n', '8e61e58e234408358ebe72e5f3a59a6fb1adb59db8e7656f72bc034a857c269d', 'python', '--version']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:435 in _test │
│ │
│ 432 │ │ try: │
│ 433 │ │ │ _ = path.write_bytes(encoded_env) │
│ 434 │ │ │ logger.debug("written conda env to {}", path) │
│ ❱ 435 │ │ │ run_command( │
│ 436 │ │ │ │ [ │
│ 437 │ │ │ │ │ CONDA_CMD, │
│ 438 │ │ │ │ │ "env", │
│ │
│ /home/runner/.local/lib/python3.12/site-packages/bioimageio/core/_resource_tests.py:198 in defau │
│ │
│ 195 │
│ 196 def default_run_command(args: Sequence[str]): │
│ 197 │ logger.info("running '{}'...", " ".join(args)) │
│ ❱ 198 │ _ = subprocess.check_call(args) │
│ 199 │
│ 200 │
│ 201 def test_description( │
│ │
│ /usr/lib/python3.12/subprocess.py:413 in check_call │
│ │
│ 410 │ │ cmd = kwargs.get("args") │
│ 411 │ │ if cmd is None: │
│ 412 │ │ │ cmd = popenargs[0] │
│ ❱ 413 │ │ raise CalledProcessError(retcode, cmd) │
│ 414 │ return 0 │
│ 415 │
│ 416 │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
CalledProcessError: Command '['conda', 'env', 'create', '--yes', '--file=/tmp/tmpsnn702v5/torchscript/env.yaml', '--name=8e61e58e234408358ebe72e5f3a59a6fb1adb59db8e7656f72bc034a857c269d', '--quiet']' returned non-zero exit status 1.